Honey is proposed to be the oldest natural sweetener and it is a standard component of several dietary patterns. Recent evidence suggests that replacing sugars, such as fructose, with honey has potential health benefits. In this study, we determined the effects of honey supplementation in mice on cardiometabolic and inflammatory markers and changes in gut microbiota and metabolomic profiles. We compared mice fed a honey diet (1 or 2 g/kg) with those fed an analog diet (mixed fructose, glucose, and sucrose (FSG) solutions) at exact dosages for one month. We found the same blood glucose fluctuating trends for honey- and FGS-fed mice. The honey diets resulted in less weight gain and fewer ballooned hepatocytes. Additionally, honey diets decreased the total serum cholesterol and TNF-α and increased the antioxidant enzyme activity. Each diet type was associated with distinct gut microbiota and metabolomics profiles. Systems biology analysis revealed that Lactococcus spp., Lachnospiraceae spp., and oleamide had the strongest correlations with lipid metabolic networks. Although in an animal model, this study provides a good understanding of the potential benefits of choosing honey rather than mixed sugars in regular dietary patterns.